Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Input file for intervals argument
Hi All, I am currently running MuTect 2 on my files. However, this is taking quite a deal of time per tumour/ normal pair analysis. I have read that using the intervals argument would decrease runtime. However, I am unsure what such a file looks like or where to get one. My data is derived from exome sequencing with exome capture being performed using Sureselect Human All Exon V5. I have downloaded the files: S04380110_AllTracks.bed, S04380110_Covered.bed, S04380110_Padded.bed, S04380110_Regions.bed, S04380110_Targets.txt and S04380110_Regions.bed. Not sure if any of these are correct file to use. Thanks for any help.